Branch: refs/heads/release_18.01
Home: https://github.com/galaxyproject/galaxy
Commit: 2f020ef9441d3eec8f0d517fe9f3412df1bfb8d5
https://github.com/galaxyproject/galaxy/commit/2f020ef9441d3eec8f0d517fe9f3…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-05 (Mon, 05 Feb 2018)
Changed paths:
M lib/galaxy/tools/parser/xml.py
Log Message:
-----------
Fix tool stdio level parsing for OOM level.
Backend was enhanced to allow this in #5196 and a new entry point to setting exit code for such exit conditions but the custom parsing wasn't updated to allow it. Thanks to @nsoranzo for the catch.
Commit: c3ada7f16973718f49ffeb1de8dc44f882ee9fd2
https://github.com/galaxyproject/galaxy/commit/c3ada7f16973718f49ffeb1de8dc…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-05 (Mon, 05 Feb 2018)
Changed paths:
M lib/galaxy/tools/parser/xml.py
Log Message:
-----------
Merge pull request #5460 from jmchilton/fix_oom_parse
[18.01] Fix tool stdio level parsing for OOM level.
Compare: https://github.com/galaxyproject/galaxy/compare/f0a8243f7d40...c3ada7f16973
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: ab3d53c5ce170855d68c955f5cb453d70989f630
https://github.com/galaxyproject/galaxy/commit/ab3d53c5ce170855d68c955f5cb4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M lib/galaxy/managers/collections.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
More options for collection deletion.
Delete button now a drop down menu (like dropdown for downloading metadata files).
- Top option just deletes the collection.
- Second option deletes the collection and attempts to delete the datasets contained within it.
- The third option deletes the collection and attempts to purge the datasets within it.
Commit: b0162ba5431097185faf641935d6ca27e11073e2
https://github.com/galaxyproject/galaxy/commit/b0162ba5431097185faf641935d6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/util/facts.py
Log Message:
-----------
Fix server_name when config is a dict.
Commit: 55b6d601a8ae5ad43a234721b2b21cc6db6ae067
https://github.com/galaxyproject/galaxy/commit/55b6d601a8ae5ad43a234721b2b2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
Log Message:
-----------
add empty href to links so the cursor is right
Commit: 8019afb8b544ef57de953d8ae23e8a45b0e15d52
https://github.com/galaxyproject/galaxy/commit/8019afb8b544ef57de953d8ae23e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
Log Message:
-----------
fix typo
Commit: 3512096a146f7d32ebc352049717df22a7c87fef
https://github.com/galaxyproject/galaxy/commit/3512096a146f7d32ebc352049717…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
Log Message:
-----------
remove unused classes and aria
Commit: dac1ba58124eb0d3b96cf6e114f6ff0e101726c8
https://github.com/galaxyproject/galaxy/commit/dac1ba58124eb0d3b96cf6e114f6…
Author: Nate Coraor <nate(a)bx.psu.edu>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/config.py
Log Message:
-----------
Fix failing integration tests for workflow handlers.
Commit: b28fb7e4d7af29ffd6db7ce2674fe2be3d6dad03
https://github.com/galaxyproject/galaxy/commit/b28fb7e4d7af29ffd6db7ce2674f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-04 (Sun, 04 Feb 2018)
Changed paths:
M client/galaxy/style/less/ui/icon-btn.less
Log Message:
-----------
change the history icon-btn selector to work with dropdowns
Commit: 2cb3af5d60d5fe08889691a8ff3b2b31038727b7
https://github.com/galaxyproject/galaxy/commit/2cb3af5d60d5fe08889691a8ff3b…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-05 (Mon, 05 Feb 2018)
Changed paths:
M lib/galaxy/config.py
M lib/galaxy/util/facts.py
Log Message:
-----------
Merge pull request #5447 from natefoo/server-name-fix
[18.01] Fix server_name when config is a dict
Commit: 0704d63d0b6353cf59153f59ab27519dc6bfc7d4
https://github.com/galaxyproject/galaxy/commit/0704d63d0b6353cf59153f59ab27…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-05 (Mon, 05 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/style/less/ui/icon-btn.less
M lib/galaxy/managers/collections.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/1801_hdca_delete' into release_18.01
Commit: f0a8243f7d4079ac406e0a2d8b0a061f1745dca1
https://github.com/galaxyproject/galaxy/commit/f0a8243f7d4079ac406e0a2d8b0a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-05 (Mon, 05 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
Log Message:
-----------
Client-format post-merge
Commit: 3a7414acaca59dc602ab3ea8092df2be9ce34258
https://github.com/galaxyproject/galaxy/commit/3a7414acaca59dc602ab3ea8092d…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-05 (Mon, 05 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/style/less/ui/icon-btn.less
M lib/galaxy/config.py
M lib/galaxy/managers/collections.py
M lib/galaxy/util/facts.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Merge remote-tracking branch 'upstream/release_18.01' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/490f67f3a0e7...3a7414acaca5
Branch: refs/heads/release_18.01
Home: https://github.com/galaxyproject/galaxy
Commit: ab3d53c5ce170855d68c955f5cb453d70989f630
https://github.com/galaxyproject/galaxy/commit/ab3d53c5ce170855d68c955f5cb4…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M lib/galaxy/managers/collections.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
More options for collection deletion.
Delete button now a drop down menu (like dropdown for downloading metadata files).
- Top option just deletes the collection.
- Second option deletes the collection and attempts to delete the datasets contained within it.
- The third option deletes the collection and attempts to purge the datasets within it.
Commit: 55b6d601a8ae5ad43a234721b2b21cc6db6ae067
https://github.com/galaxyproject/galaxy/commit/55b6d601a8ae5ad43a234721b2b2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
Log Message:
-----------
add empty href to links so the cursor is right
Commit: 8019afb8b544ef57de953d8ae23e8a45b0e15d52
https://github.com/galaxyproject/galaxy/commit/8019afb8b544ef57de953d8ae23e…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
Log Message:
-----------
fix typo
Commit: 3512096a146f7d32ebc352049717df22a7c87fef
https://github.com/galaxyproject/galaxy/commit/3512096a146f7d32ebc352049717…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
Log Message:
-----------
remove unused classes and aria
Commit: b28fb7e4d7af29ffd6db7ce2674fe2be3d6dad03
https://github.com/galaxyproject/galaxy/commit/b28fb7e4d7af29ffd6db7ce2674f…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-04 (Sun, 04 Feb 2018)
Changed paths:
M client/galaxy/style/less/ui/icon-btn.less
Log Message:
-----------
change the history icon-btn selector to work with dropdowns
Commit: 0704d63d0b6353cf59153f59ab27519dc6bfc7d4
https://github.com/galaxyproject/galaxy/commit/0704d63d0b6353cf59153f59ab27…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-05 (Mon, 05 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/dataset/dataset-li.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
M client/galaxy/style/less/ui/icon-btn.less
M lib/galaxy/managers/collections.py
M lib/galaxy/webapps/galaxy/api/history_contents.py
Log Message:
-----------
Merge remote-tracking branch 'jmchilton/1801_hdca_delete' into release_18.01
Commit: f0a8243f7d4079ac406e0a2d8b0a061f1745dca1
https://github.com/galaxyproject/galaxy/commit/f0a8243f7d4079ac406e0a2d8b0a…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-05 (Mon, 05 Feb 2018)
Changed paths:
M client/galaxy/scripts/mvc/collection/collection-model.js
M client/galaxy/scripts/mvc/history/hdca-li-edit.js
Log Message:
-----------
Client-format post-merge
Compare: https://github.com/galaxyproject/galaxy/compare/2cb3af5d60d5...f0a8243f7d40
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 5958d173c44e20e8860f90498f01cf2e6f510cf9
https://github.com/galaxyproject/galaxy/commit/5958d173c44e20e8860f90498f01…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M .gitignore
R static/scripts/admin.toolshed.js
R static/scripts/bundled/admin.bundled.js
R static/scripts/bundled/analysis.bundled.js
R static/scripts/bundled/extended.bundled.js
R static/scripts/bundled/libs.bundled.js
R static/scripts/bundled/login.bundled.js
R static/scripts/galaxy.interactive_environments.js
R static/scripts/galaxy.js
R static/scripts/galaxy.library.js
R static/scripts/galaxy.pages.js
R static/scripts/i18n.js
R static/scripts/layout/generic-nav-view.js
R static/scripts/layout/masthead.js
R static/scripts/layout/menu.js
R static/scripts/layout/modal.js
R static/scripts/layout/page.js
R static/scripts/layout/panel.js
R static/scripts/layout/router.js
R static/scripts/layout/scratchbook.js
R static/scripts/legacy/grid/grid-model.js
R static/scripts/legacy/grid/grid-template.js
R static/scripts/legacy/grid/grid-view.js
R static/scripts/libs/backbone.js
R static/scripts/libs/bbi/bigwig.js
R static/scripts/libs/bbi/jquery-ajax-native.js
R static/scripts/libs/bbi/jszlib.js
R static/scripts/libs/bbi/spans.js
R static/scripts/libs/bibtexParse.js
R static/scripts/libs/bootstrap-tour.js
R static/scripts/libs/bootstrap.js
R static/scripts/libs/d3.js
R static/scripts/libs/farbtastic.js
R static/scripts/libs/jquery.sparklines.js
R static/scripts/libs/jquery/jquery-ui.js
R static/scripts/libs/jquery/jquery.autocomplete.js
R static/scripts/libs/jquery/jquery.complexify.js
R static/scripts/libs/jquery/jquery.cookie.js
R static/scripts/libs/jquery/jquery.dynatree.js
R static/scripts/libs/jquery/jquery.event.drag.js
R static/scripts/libs/jquery/jquery.event.drop.js
R static/scripts/libs/jquery/jquery.event.hover.js
R static/scripts/libs/jquery/jquery.form.js
R static/scripts/libs/jquery/jquery.js
R static/scripts/libs/jquery/jquery.migrate.js
R static/scripts/libs/jquery/jquery.mousewheel.js
R static/scripts/libs/jquery/jquery.rating.js
R static/scripts/libs/jquery/jquery.wymeditor.js
R static/scripts/libs/jquery/jstorage.js
R static/scripts/libs/jquery/jstree.js
R static/scripts/libs/jquery/select2.js
R static/scripts/libs/raven.js
R static/scripts/libs/require.js
R static/scripts/libs/toastr.js
R static/scripts/libs/underscore.js
R static/scripts/mvc/annotation.js
R static/scripts/mvc/base-mvc.js
R static/scripts/mvc/base/controlled-fetch-collection.js
R static/scripts/mvc/collection/base-creator.js
R static/scripts/mvc/collection/collection-li-edit.js
R static/scripts/mvc/collection/collection-li.js
R static/scripts/mvc/collection/collection-model.js
R static/scripts/mvc/collection/collection-view-edit.js
R static/scripts/mvc/collection/collection-view.js
R static/scripts/mvc/collection/list-collection-creator.js
R static/scripts/mvc/collection/list-of-pairs-collection-creator.js
R static/scripts/mvc/collection/pair-collection-creator.js
R static/scripts/mvc/dataset/data.js
R static/scripts/mvc/dataset/dataset-choice.js
R static/scripts/mvc/dataset/dataset-edit-attributes.js
R static/scripts/mvc/dataset/dataset-error.js
R static/scripts/mvc/dataset/dataset-li-edit.js
R static/scripts/mvc/dataset/dataset-li.js
R static/scripts/mvc/dataset/dataset-list.js
R static/scripts/mvc/dataset/dataset-model.js
R static/scripts/mvc/dataset/states.js
R static/scripts/mvc/form/form-data.js
R static/scripts/mvc/form/form-input.js
R static/scripts/mvc/form/form-parameters.js
R static/scripts/mvc/form/form-repeat.js
R static/scripts/mvc/form/form-section.js
R static/scripts/mvc/form/form-view.js
R static/scripts/mvc/form/form-wrapper.js
R static/scripts/mvc/grid/grid-model.js
R static/scripts/mvc/grid/grid-shared.js
R static/scripts/mvc/grid/grid-template.js
R static/scripts/mvc/grid/grid-view.js
R static/scripts/mvc/history/copy-dialog.js
R static/scripts/mvc/history/hda-li-edit.js
R static/scripts/mvc/history/hda-li.js
R static/scripts/mvc/history/hda-model.js
R static/scripts/mvc/history/hdca-li-edit.js
R static/scripts/mvc/history/hdca-li.js
R static/scripts/mvc/history/hdca-model.js
R static/scripts/mvc/history/history-content-model.js
R static/scripts/mvc/history/history-contents.js
R static/scripts/mvc/history/history-item-li.js
R static/scripts/mvc/history/history-list.js
R static/scripts/mvc/history/history-model.js
R static/scripts/mvc/history/history-preferences.js
R static/scripts/mvc/history/history-structure-view.js
R static/scripts/mvc/history/history-view-annotated.js
R static/scripts/mvc/history/history-view-edit-current.js
R static/scripts/mvc/history/history-view-edit.js
R static/scripts/mvc/history/history-view.js
R static/scripts/mvc/history/job-dag.js
R static/scripts/mvc/history/job-states-model.js
R static/scripts/mvc/history/multi-panel.js
R static/scripts/mvc/history/options-menu.js
R static/scripts/mvc/job/job-li.js
R static/scripts/mvc/job/job-model.js
R static/scripts/mvc/job/job-params.js
R static/scripts/mvc/lazy/lazy-limited.js
R static/scripts/mvc/library/library-dataset-view.js
R static/scripts/mvc/library/library-folder-view.js
R static/scripts/mvc/library/library-folderlist-view.js
R static/scripts/mvc/library/library-folderrow-view.js
R static/scripts/mvc/library/library-foldertoolbar-view.js
R static/scripts/mvc/library/library-library-view.js
R static/scripts/mvc/library/library-librarylist-view.js
R static/scripts/mvc/library/library-libraryrow-view.js
R static/scripts/mvc/library/library-librarytoolbar-view.js
R static/scripts/mvc/library/library-model.js
R static/scripts/mvc/library/library-util.js
R static/scripts/mvc/list/list-item.js
R static/scripts/mvc/list/list-view.js
R static/scripts/mvc/tag.js
R static/scripts/mvc/tool/tool-form-base.js
R static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form.js
R static/scripts/mvc/tool/tool-genomespace.js
R static/scripts/mvc/tool/tools.js
R static/scripts/mvc/toolshed/categories-view.js
R static/scripts/mvc/toolshed/repo-queue-view.js
R static/scripts/mvc/toolshed/repo-status-view.js
R static/scripts/mvc/toolshed/repositories-view.js
R static/scripts/mvc/toolshed/repository-queue-view.js
R static/scripts/mvc/toolshed/repository-view.js
R static/scripts/mvc/toolshed/shed-list-view.js
R static/scripts/mvc/toolshed/toolshed-model.js
R static/scripts/mvc/toolshed/util.js
R static/scripts/mvc/toolshed/workflows-view.js
R static/scripts/mvc/tours.js
R static/scripts/mvc/ui/error-modal.js
R static/scripts/mvc/ui/icon-button.js
R static/scripts/mvc/ui/popup-menu.js
R static/scripts/mvc/ui/ui-buttons.js
R static/scripts/mvc/ui/ui-color-picker.js
R static/scripts/mvc/ui/ui-drilldown.js
R static/scripts/mvc/ui/ui-frames.js
R static/scripts/mvc/ui/ui-list.js
R static/scripts/mvc/ui/ui-misc.js
R static/scripts/mvc/ui/ui-modal.js
R static/scripts/mvc/ui/ui-options.js
R static/scripts/mvc/ui/ui-popover.js
R static/scripts/mvc/ui/ui-portlet.js
R static/scripts/mvc/ui/ui-select-content.js
R static/scripts/mvc/ui/ui-select-default.js
R static/scripts/mvc/ui/ui-select-ftp.js
R static/scripts/mvc/ui/ui-select-genomespace.js
R static/scripts/mvc/ui/ui-select-library.js
R static/scripts/mvc/ui/ui-select.js
R static/scripts/mvc/ui/ui-slider.js
R static/scripts/mvc/ui/ui-table.js
R static/scripts/mvc/ui/ui-tabs.js
R static/scripts/mvc/ui/ui-thumbnails.js
R static/scripts/mvc/upload/collection/collection-row.js
R static/scripts/mvc/upload/collection/collection-view.js
R static/scripts/mvc/upload/composite/composite-row.js
R static/scripts/mvc/upload/composite/composite-view.js
R static/scripts/mvc/upload/default/default-row.js
R static/scripts/mvc/upload/default/default-view.js
R static/scripts/mvc/upload/upload-button.js
R static/scripts/mvc/upload/upload-extension.js
R static/scripts/mvc/upload/upload-ftp.js
R static/scripts/mvc/upload/upload-model.js
R static/scripts/mvc/upload/upload-settings.js
R static/scripts/mvc/upload/upload-view.js
R static/scripts/mvc/user/user-custom-builds.js
R static/scripts/mvc/user/user-model.js
R static/scripts/mvc/user/user-preferences.js
R static/scripts/mvc/user/user-quotameter.js
R static/scripts/mvc/visualization/visualization-model.js
R static/scripts/mvc/webhooks.js
R static/scripts/mvc/workflow/workflow-canvas.js
R static/scripts/mvc/workflow/workflow-connector.js
R static/scripts/mvc/workflow/workflow-forms.js
R static/scripts/mvc/workflow/workflow-icons.js
R static/scripts/mvc/workflow/workflow-manager.js
R static/scripts/mvc/workflow/workflow-model.js
R static/scripts/mvc/workflow/workflow-node.js
R static/scripts/mvc/workflow/workflow-terminals.js
R static/scripts/mvc/workflow/workflow-view-data.js
R static/scripts/mvc/workflow/workflow-view-node.js
R static/scripts/mvc/workflow/workflow-view-terminals.js
R static/scripts/mvc/workflow/workflow-view.js
R static/scripts/mvc/workflow/workflow.js
R static/scripts/nls/de/locale.js
R static/scripts/nls/es/locale.js
R static/scripts/nls/fr/locale.js
R static/scripts/nls/ja/locale.js
R static/scripts/nls/locale.js
R static/scripts/nls/zh/locale.js
R static/scripts/onload.js
R static/scripts/polyfills.js
R static/scripts/reports/run_stats.js
R static/scripts/toolshed/groups/group-detail-view.js
R static/scripts/toolshed/groups/group-list-view.js
R static/scripts/toolshed/groups/group-listrow-view.js
R static/scripts/toolshed/groups/group-model.js
R static/scripts/toolshed/toolshed.groups.js
R static/scripts/ui/autocom_tagging.js
R static/scripts/ui/editable-text.js
R static/scripts/ui/fa-icon-button.js
R static/scripts/ui/filter-control.js
R static/scripts/ui/hoverhighlight.js
R static/scripts/ui/loading-indicator.js
R static/scripts/ui/mode-button.js
R static/scripts/ui/pagination.js
R static/scripts/ui/peek-column-selector.js
R static/scripts/ui/popupmenu.js
R static/scripts/ui/scroll-panel.js
R static/scripts/ui/search-input.js
R static/scripts/utils/add-logging.js
R static/scripts/utils/ajax-queue.js
R static/scripts/utils/async-save-text.js
R static/scripts/utils/config.js
R static/scripts/utils/deferred.js
R static/scripts/utils/graph.js
R static/scripts/utils/levenshtein.js
R static/scripts/utils/localization.js
R static/scripts/utils/metrics-logger.js
R static/scripts/utils/natural-sort.js
R static/scripts/utils/query-string-parsing.js
R static/scripts/utils/uploadbox.js
R static/scripts/utils/utils.js
R static/scripts/viz/bbi-data-manager.js
R static/scripts/viz/circster.js
R static/scripts/viz/phyloviz.js
R static/scripts/viz/sweepster.js
R static/scripts/viz/trackster.js
R static/scripts/viz/trackster/filters.js
R static/scripts/viz/trackster/painters.js
R static/scripts/viz/trackster/slotting.js
R static/scripts/viz/trackster/tracks.js
R static/scripts/viz/trackster/util.js
R static/scripts/viz/visualization.js
R static/scripts/viz/viz_views.js
Log Message:
-----------
Remove static/scripts/* from the dev branch, add to .gitignore. These
will be manually added back to release branches along with any other
artifacts for distribution. This slight release-time burden will (per
feedback from multiple developers) make it easier to manage changes to
-dev.
Commit: 29a1bf05e68a54c4fc9242e86ec5d27c8ac1db1a
https://github.com/galaxyproject/galaxy/commit/29a1bf05e68a54c4fc9242e86ec5…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-01 (Thu, 01 Feb 2018)
Changed paths:
M .gitignore
Log Message:
-----------
Remove redundant subdir rules.
Commit: 204bb0e8fdf5ff10696e03c51c6805a62de79813
https://github.com/galaxyproject/galaxy/commit/204bb0e8fdf5ff10696e03c51c68…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-05 (Mon, 05 Feb 2018)
Changed paths:
M .gitignore
R static/scripts/admin.toolshed.js
R static/scripts/bundled/admin.bundled.js
R static/scripts/bundled/analysis.bundled.js
R static/scripts/bundled/extended.bundled.js
R static/scripts/bundled/libs.bundled.js
R static/scripts/bundled/login.bundled.js
R static/scripts/galaxy.interactive_environments.js
R static/scripts/galaxy.js
R static/scripts/galaxy.library.js
R static/scripts/galaxy.pages.js
R static/scripts/i18n.js
R static/scripts/layout/generic-nav-view.js
R static/scripts/layout/masthead.js
R static/scripts/layout/menu.js
R static/scripts/layout/modal.js
R static/scripts/layout/page.js
R static/scripts/layout/panel.js
R static/scripts/layout/router.js
R static/scripts/layout/scratchbook.js
R static/scripts/legacy/grid/grid-model.js
R static/scripts/legacy/grid/grid-template.js
R static/scripts/legacy/grid/grid-view.js
R static/scripts/libs/backbone.js
R static/scripts/libs/bbi/bigwig.js
R static/scripts/libs/bbi/jquery-ajax-native.js
R static/scripts/libs/bbi/jszlib.js
R static/scripts/libs/bbi/spans.js
R static/scripts/libs/bibtexParse.js
R static/scripts/libs/bootstrap-tour.js
R static/scripts/libs/bootstrap.js
R static/scripts/libs/d3.js
R static/scripts/libs/farbtastic.js
R static/scripts/libs/jquery.sparklines.js
R static/scripts/libs/jquery/jquery-ui.js
R static/scripts/libs/jquery/jquery.autocomplete.js
R static/scripts/libs/jquery/jquery.complexify.js
R static/scripts/libs/jquery/jquery.cookie.js
R static/scripts/libs/jquery/jquery.dynatree.js
R static/scripts/libs/jquery/jquery.event.drag.js
R static/scripts/libs/jquery/jquery.event.drop.js
R static/scripts/libs/jquery/jquery.event.hover.js
R static/scripts/libs/jquery/jquery.form.js
R static/scripts/libs/jquery/jquery.js
R static/scripts/libs/jquery/jquery.migrate.js
R static/scripts/libs/jquery/jquery.mousewheel.js
R static/scripts/libs/jquery/jquery.rating.js
R static/scripts/libs/jquery/jquery.wymeditor.js
R static/scripts/libs/jquery/jstorage.js
R static/scripts/libs/jquery/jstree.js
R static/scripts/libs/jquery/select2.js
R static/scripts/libs/raven.js
R static/scripts/libs/require.js
R static/scripts/libs/toastr.js
R static/scripts/libs/underscore.js
R static/scripts/mvc/annotation.js
R static/scripts/mvc/base-mvc.js
R static/scripts/mvc/base/controlled-fetch-collection.js
R static/scripts/mvc/collection/base-creator.js
R static/scripts/mvc/collection/collection-li-edit.js
R static/scripts/mvc/collection/collection-li.js
R static/scripts/mvc/collection/collection-model.js
R static/scripts/mvc/collection/collection-view-edit.js
R static/scripts/mvc/collection/collection-view.js
R static/scripts/mvc/collection/list-collection-creator.js
R static/scripts/mvc/collection/list-of-pairs-collection-creator.js
R static/scripts/mvc/collection/pair-collection-creator.js
R static/scripts/mvc/dataset/data.js
R static/scripts/mvc/dataset/dataset-choice.js
R static/scripts/mvc/dataset/dataset-edit-attributes.js
R static/scripts/mvc/dataset/dataset-error.js
R static/scripts/mvc/dataset/dataset-li-edit.js
R static/scripts/mvc/dataset/dataset-li.js
R static/scripts/mvc/dataset/dataset-list.js
R static/scripts/mvc/dataset/dataset-model.js
R static/scripts/mvc/dataset/states.js
R static/scripts/mvc/form/form-data.js
R static/scripts/mvc/form/form-input.js
R static/scripts/mvc/form/form-parameters.js
R static/scripts/mvc/form/form-repeat.js
R static/scripts/mvc/form/form-section.js
R static/scripts/mvc/form/form-view.js
R static/scripts/mvc/form/form-wrapper.js
R static/scripts/mvc/grid/grid-model.js
R static/scripts/mvc/grid/grid-shared.js
R static/scripts/mvc/grid/grid-template.js
R static/scripts/mvc/grid/grid-view.js
R static/scripts/mvc/history/copy-dialog.js
R static/scripts/mvc/history/hda-li-edit.js
R static/scripts/mvc/history/hda-li.js
R static/scripts/mvc/history/hda-model.js
R static/scripts/mvc/history/hdca-li-edit.js
R static/scripts/mvc/history/hdca-li.js
R static/scripts/mvc/history/hdca-model.js
R static/scripts/mvc/history/history-content-model.js
R static/scripts/mvc/history/history-contents.js
R static/scripts/mvc/history/history-item-li.js
R static/scripts/mvc/history/history-list.js
R static/scripts/mvc/history/history-model.js
R static/scripts/mvc/history/history-preferences.js
R static/scripts/mvc/history/history-structure-view.js
R static/scripts/mvc/history/history-view-annotated.js
R static/scripts/mvc/history/history-view-edit-current.js
R static/scripts/mvc/history/history-view-edit.js
R static/scripts/mvc/history/history-view.js
R static/scripts/mvc/history/job-dag.js
R static/scripts/mvc/history/job-states-model.js
R static/scripts/mvc/history/multi-panel.js
R static/scripts/mvc/history/options-menu.js
R static/scripts/mvc/job/job-li.js
R static/scripts/mvc/job/job-model.js
R static/scripts/mvc/job/job-params.js
R static/scripts/mvc/lazy/lazy-limited.js
R static/scripts/mvc/library/library-dataset-view.js
R static/scripts/mvc/library/library-folder-view.js
R static/scripts/mvc/library/library-folderlist-view.js
R static/scripts/mvc/library/library-folderrow-view.js
R static/scripts/mvc/library/library-foldertoolbar-view.js
R static/scripts/mvc/library/library-library-view.js
R static/scripts/mvc/library/library-librarylist-view.js
R static/scripts/mvc/library/library-libraryrow-view.js
R static/scripts/mvc/library/library-librarytoolbar-view.js
R static/scripts/mvc/library/library-model.js
R static/scripts/mvc/library/library-util.js
R static/scripts/mvc/list/list-item.js
R static/scripts/mvc/list/list-view.js
R static/scripts/mvc/tag.js
R static/scripts/mvc/tool/tool-form-base.js
R static/scripts/mvc/tool/tool-form-composite.js
R static/scripts/mvc/tool/tool-form.js
R static/scripts/mvc/tool/tool-genomespace.js
R static/scripts/mvc/tool/tools.js
R static/scripts/mvc/toolshed/categories-view.js
R static/scripts/mvc/toolshed/repo-queue-view.js
R static/scripts/mvc/toolshed/repo-status-view.js
R static/scripts/mvc/toolshed/repositories-view.js
R static/scripts/mvc/toolshed/repository-queue-view.js
R static/scripts/mvc/toolshed/repository-view.js
R static/scripts/mvc/toolshed/shed-list-view.js
R static/scripts/mvc/toolshed/toolshed-model.js
R static/scripts/mvc/toolshed/util.js
R static/scripts/mvc/toolshed/workflows-view.js
R static/scripts/mvc/tours.js
R static/scripts/mvc/ui/error-modal.js
R static/scripts/mvc/ui/icon-button.js
R static/scripts/mvc/ui/popup-menu.js
R static/scripts/mvc/ui/ui-buttons.js
R static/scripts/mvc/ui/ui-color-picker.js
R static/scripts/mvc/ui/ui-drilldown.js
R static/scripts/mvc/ui/ui-frames.js
R static/scripts/mvc/ui/ui-list.js
R static/scripts/mvc/ui/ui-misc.js
R static/scripts/mvc/ui/ui-modal.js
R static/scripts/mvc/ui/ui-options.js
R static/scripts/mvc/ui/ui-popover.js
R static/scripts/mvc/ui/ui-portlet.js
R static/scripts/mvc/ui/ui-select-content.js
R static/scripts/mvc/ui/ui-select-default.js
R static/scripts/mvc/ui/ui-select-ftp.js
R static/scripts/mvc/ui/ui-select-genomespace.js
R static/scripts/mvc/ui/ui-select-library.js
R static/scripts/mvc/ui/ui-select.js
R static/scripts/mvc/ui/ui-slider.js
R static/scripts/mvc/ui/ui-table.js
R static/scripts/mvc/ui/ui-tabs.js
R static/scripts/mvc/ui/ui-thumbnails.js
R static/scripts/mvc/upload/collection/collection-row.js
R static/scripts/mvc/upload/collection/collection-view.js
R static/scripts/mvc/upload/composite/composite-row.js
R static/scripts/mvc/upload/composite/composite-view.js
R static/scripts/mvc/upload/default/default-row.js
R static/scripts/mvc/upload/default/default-view.js
R static/scripts/mvc/upload/upload-button.js
R static/scripts/mvc/upload/upload-extension.js
R static/scripts/mvc/upload/upload-ftp.js
R static/scripts/mvc/upload/upload-model.js
R static/scripts/mvc/upload/upload-settings.js
R static/scripts/mvc/upload/upload-view.js
R static/scripts/mvc/user/user-custom-builds.js
R static/scripts/mvc/user/user-model.js
R static/scripts/mvc/user/user-preferences.js
R static/scripts/mvc/user/user-quotameter.js
R static/scripts/mvc/visualization/visualization-model.js
R static/scripts/mvc/webhooks.js
R static/scripts/mvc/workflow/workflow-canvas.js
R static/scripts/mvc/workflow/workflow-connector.js
R static/scripts/mvc/workflow/workflow-forms.js
R static/scripts/mvc/workflow/workflow-icons.js
R static/scripts/mvc/workflow/workflow-manager.js
R static/scripts/mvc/workflow/workflow-model.js
R static/scripts/mvc/workflow/workflow-node.js
R static/scripts/mvc/workflow/workflow-terminals.js
R static/scripts/mvc/workflow/workflow-view-data.js
R static/scripts/mvc/workflow/workflow-view-node.js
R static/scripts/mvc/workflow/workflow-view-terminals.js
R static/scripts/mvc/workflow/workflow-view.js
R static/scripts/mvc/workflow/workflow.js
R static/scripts/nls/de/locale.js
R static/scripts/nls/es/locale.js
R static/scripts/nls/fr/locale.js
R static/scripts/nls/ja/locale.js
R static/scripts/nls/locale.js
R static/scripts/nls/zh/locale.js
R static/scripts/onload.js
R static/scripts/polyfills.js
R static/scripts/reports/run_stats.js
R static/scripts/toolshed/groups/group-detail-view.js
R static/scripts/toolshed/groups/group-list-view.js
R static/scripts/toolshed/groups/group-listrow-view.js
R static/scripts/toolshed/groups/group-model.js
R static/scripts/toolshed/toolshed.groups.js
R static/scripts/ui/autocom_tagging.js
R static/scripts/ui/editable-text.js
R static/scripts/ui/fa-icon-button.js
R static/scripts/ui/filter-control.js
R static/scripts/ui/hoverhighlight.js
R static/scripts/ui/loading-indicator.js
R static/scripts/ui/mode-button.js
R static/scripts/ui/pagination.js
R static/scripts/ui/peek-column-selector.js
R static/scripts/ui/popupmenu.js
R static/scripts/ui/scroll-panel.js
R static/scripts/ui/search-input.js
R static/scripts/utils/add-logging.js
R static/scripts/utils/ajax-queue.js
R static/scripts/utils/async-save-text.js
R static/scripts/utils/config.js
R static/scripts/utils/deferred.js
R static/scripts/utils/graph.js
R static/scripts/utils/levenshtein.js
R static/scripts/utils/localization.js
R static/scripts/utils/metrics-logger.js
R static/scripts/utils/natural-sort.js
R static/scripts/utils/query-string-parsing.js
R static/scripts/utils/uploadbox.js
R static/scripts/utils/utils.js
R static/scripts/viz/bbi-data-manager.js
R static/scripts/viz/circster.js
R static/scripts/viz/phyloviz.js
R static/scripts/viz/sweepster.js
R static/scripts/viz/trackster.js
R static/scripts/viz/trackster/filters.js
R static/scripts/viz/trackster/painters.js
R static/scripts/viz/trackster/slotting.js
R static/scripts/viz/trackster/tracks.js
R static/scripts/viz/trackster/util.js
R static/scripts/viz/visualization.js
R static/scripts/viz/viz_views.js
Log Message:
-----------
Merge pull request #5434 from dannon/static_scripts_dev_removal
Remove static/scripts/* from the dev branch, add to .gitignore.
Compare: https://github.com/galaxyproject/galaxy/compare/3864a1763ffa...204bb0e8fdf5
Branch: refs/heads/dev
Home: https://github.com/galaxyproject/galaxy
Commit: 8e32e93d6d8e048cbc77cb94f7c97b5ae0cfc6d6
https://github.com/galaxyproject/galaxy/commit/8e32e93d6d8e048cbc77cb94f7c9…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-02 (Fri, 02 Feb 2018)
Changed paths:
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Implement more collection workflow post job actions.
Implement hide, delete, add tag, and remove tag for output collections and mapped over collections.
Fixes https://github.com/galaxyproject/galaxy/issues/1680.
Commit: 5aed347c3025ad061c572c6a2bbdf53a7626d3cc
https://github.com/galaxyproject/galaxy/commit/5aed347c3025ad061c572c6a2bbd…
Author: Marius van den Beek <m.vandenbeek(a)gmail.com>
Date: 2018-02-03 (Sat, 03 Feb 2018)
Changed paths:
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/workflow/modules.py
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Merge pull request #5418 from jmchilton/collection_pja
[18.01] Implement more intuitive collection PJA
Commit: 935b8c948cf4e47d1ea08fbe51332b7c6f15caa0
https://github.com/galaxyproject/galaxy/commit/935b8c948cf4e47d1ea08fbe5133…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-02-03 (Sat, 03 Feb 2018)
Changed paths:
M .ci/jenkins/api/run_tests.sh
Log Message:
-----------
Add --skip_flakey_fails flag to CI script for API tests
xref. https://github.com/galaxyproject/galaxy/pull/5286#issuecomment-358404551
and following comments.
Commit: 1bd8c4fd26b6dbb2824922cbc7f24ab9e8929bfe
https://github.com/galaxyproject/galaxy/commit/1bd8c4fd26b6dbb2824922cbc7f2…
Author: Martin Cech <marten(a)bx.psu.edu>
Date: 2018-02-03 (Sat, 03 Feb 2018)
Changed paths:
M .ci/jenkins/api/run_tests.sh
Log Message:
-----------
Merge pull request #5455 from jmchilton/backport_flakey
[18.01] Backport: Add --skip_flakey_fails flag to CI script for API tests
Commit: 7bbc46658a77d74a2447095b61b28e6e4ca32e06
https://github.com/galaxyproject/galaxy/commit/7bbc46658a77d74a2447095b61b2…
Author: mvdbeek <m.vandenbeek(a)gmail.com>
Date: 2018-02-03 (Sat, 03 Feb 2018)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Fix setting job failure exception
This can happen when the job's tool is unavailble and
outputs_to_working_directory is activated.
Fixes https://github.com/galaxyproject/galaxy/issues/5424.
Commit: f99299f8332a75a6075f49176770078be9cda571
https://github.com/galaxyproject/galaxy/commit/f99299f8332a75a6075f49176770…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-03 (Sat, 03 Feb 2018)
Changed paths:
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/tools/execute.py
Log Message:
-----------
Pre-compute more collection state during mapping.
Still dealing with fallout from 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03. After that commit we were treating structured_like collections like collections with unknown structure and not dealing with collection_type_source information at all when building backbones for new collections during mapping.
Commit: 51e030f4f3b608710adbba9ed4647db3d20196cb
https://github.com/galaxyproject/galaxy/commit/51e030f4f3b608710adbba9ed464…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-03 (Sat, 03 Feb 2018)
Changed paths:
M test/api/test_tools.py
Log Message:
-----------
Bring in @mvdbeek's test cases from #5431.
Commit: b2e8d891b7ca7e24aaf86b6e559356e7d62f3373
https://github.com/galaxyproject/galaxy/commit/b2e8d891b7ca7e24aaf86b6e5593…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-03 (Sat, 03 Feb 2018)
Changed paths:
M lib/galaxy/jobs/__init__.py
Log Message:
-----------
Merge pull request #5456 from mvdbeek/fail_job_fix_when_tool_unavailable
Fix setting job failure exception
Commit: 207f5faba0ab70747c70de2d8d66a16ee2b00ecb
https://github.com/galaxyproject/galaxy/commit/207f5faba0ab70747c70de2d8d66…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-04 (Sun, 04 Feb 2018)
Changed paths:
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/tools/execute.py
M test/api/test_tools.py
Log Message:
-----------
Merge pull request #5449 from jmchilton/collection_mapping_fixes
[18.01] Collection mapping fixes for regression in 18.01.
Commit: 3864a1763ffa101384314090066c671bca5ba23d
https://github.com/galaxyproject/galaxy/commit/3864a1763ffa101384314090066c…
Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk>
Date: 2018-02-05 (Mon, 05 Feb 2018)
Changed paths:
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/jobs/__init__.py
M lib/galaxy/jobs/actions/post.py
M lib/galaxy/tools/execute.py
M lib/galaxy/workflow/modules.py
M test/api/test_tools.py
M test/api/test_workflows.py
M test/base/workflows_format_2/converter.py
Log Message:
-----------
Merge branch 'release_18.01' into dev
Compare: https://github.com/galaxyproject/galaxy/compare/f8d21f098af2...3864a1763ffa
Branch: refs/heads/release_18.01
Home: https://github.com/galaxyproject/galaxy
Commit: f99299f8332a75a6075f49176770078be9cda571
https://github.com/galaxyproject/galaxy/commit/f99299f8332a75a6075f49176770…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-03 (Sat, 03 Feb 2018)
Changed paths:
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/tools/execute.py
Log Message:
-----------
Pre-compute more collection state during mapping.
Still dealing with fallout from 78babab6455f4cd1c51aed0b1ddf6b4b29ad6d03. After that commit we were treating structured_like collections like collections with unknown structure and not dealing with collection_type_source information at all when building backbones for new collections during mapping.
Commit: 51e030f4f3b608710adbba9ed4647db3d20196cb
https://github.com/galaxyproject/galaxy/commit/51e030f4f3b608710adbba9ed464…
Author: John Chilton <jmchilton(a)gmail.com>
Date: 2018-02-03 (Sat, 03 Feb 2018)
Changed paths:
M test/api/test_tools.py
Log Message:
-----------
Bring in @mvdbeek's test cases from #5431.
Commit: 207f5faba0ab70747c70de2d8d66a16ee2b00ecb
https://github.com/galaxyproject/galaxy/commit/207f5faba0ab70747c70de2d8d66…
Author: Dannon Baker <dannon.baker(a)gmail.com>
Date: 2018-02-04 (Sun, 04 Feb 2018)
Changed paths:
M lib/galaxy/dataset_collections/structure.py
M lib/galaxy/tools/execute.py
M test/api/test_tools.py
Log Message:
-----------
Merge pull request #5449 from jmchilton/collection_mapping_fixes
[18.01] Collection mapping fixes for regression in 18.01.
Compare: https://github.com/galaxyproject/galaxy/compare/b2e8d891b7ca...207f5faba0ab